Here's the deal as I see it. The #1 thing auto makers have done for 20 years is design cars so they don't create MPG sucking vortexes behind their cars. Your Honda was designed so the air coming off the sides and roof create a smooth linear air flow with out a lot of swirling about. Anything you add to you car will only upset this balance and decrease efficiency. Look at the sedans with insane CD's, the new Mazda 3 .255 CD, and Benz CLA .23 CD.
The 2 things that I take away from these 2 designs is the long sweeping top arch of a line from the base of the front windscreen to the base of the back glass, with only a slight break to the trunk lip. The other is the straight-up front grills, pushing as much air around the sides as possible.
Back to your Civic, I think the only hope you might have is to make whatever you do on the back work is make sure whatever you do goes all the way back. The Kamm thing to the trunk extension break I think is your issue. But however you craft the back, you'll never be able to tell how that is interacting with the air coming around the sides and it is improbable that you'll get it nailed without a wind tunnel and passel of engineers.
Don't mean to be a downer, these are just the thoughts I had when I was contemplating modifying my 04 Sedan, as always YMMV and I could be 100% wrong. (well maybe 95%)